Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006854.1 Corchorus capsularis cultivar CVL-1 contig06875, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14601
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:716 original size:15 final size:16
Alignment explanation
Indices: 684--717 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
674 AAAGAAGAAT
*
684 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
700 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
715 TAA
1 TAA
718 GAGAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:2032 original size:19 final size:18
Alignment explanation
Indices: 1999--2034 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1989 TTGAAATAAT
*
1999 TCTTCAATGATCTTCAAA
1 TCTTCAATAATCTTCAAA
2017 TCTTCAAATAATCTTCAA
1 TCTTC-AATAATCTTCAA
2035 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:3999 original size:33 final size:33
Alignment explanation
Indices: 3921--4025 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
3911 TTGCAAAGAG
* * * *
3921 TGTTTTAGATGTTGTTTGCAATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGACACTAAATC
** *
3954 TAATTT-GAGTGTTTTTTGCGATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGACACTAAATC
* *
3987 TGTTTTAGGTGTTGTTTGTGATTACACTAAATC
1 TGTTTTAGGTGTTGTTTGCGATGACACTAAATC
4020 TGTTTT
1 TGTTTT
4026 GGATGCTAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 1 0.02
33 56 0.97
34 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGACACTAAATC
Found at i:4039 original size:33 final size:33
Alignment explanation
Indices: 3973--4061 Score: 94
Period size: 33 Copynumber: 2.7 Consensus size: 33
3963 TGTTTTTTGC
* **
3973 GATG-ACACTAAATCTGTTTTAGGTGTTGTTTGT
1 GATGAACACTAAATCTGTTTT-GGTGCTAATTGT
*
4006 GAT-TACACTAAATCTGTTTTGGATGCTAATTGT
1 GATGAACACTAAATCTGTTTTGG-TGCTAATTGT
*
4039 GATGAAAAC-AAATCTGTTTTGGT
1 GATGAACACTAAATCTGTTTTGGT
4062 TCATCATAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
32 3 0.06
33 42 0.88
34 3 0.06
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (33 bp):
GATGAACACTAAATCTGTTTTGGTGCTAATTGT
Found at i:4508 original size:30 final size:30
Alignment explanation
Indices: 4472--4559 Score: 151
Period size: 30 Copynumber: 2.9 Consensus size: 30
4462 CAAGGGGGAA
4472 GGAATGATGCGCCTAAGGGTTATCATGGAG
1 GGAATGATGCGCCTAAGGGTTATCATGGAG
4502 GGAATGATGCGCCTAAGGGTTATCATGGAG
1 GGAATGATGCGCCTAAGGGTTATCATGGAG
*
4532 GGAATGATGCGCC-AAGGACTTATCATGG
1 GGAATGATGCGCCTAAGG-GTTATCATGG
4560 GCTTGAAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 4 0.07
30 52 0.93
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.23
Consensus pattern (30 bp):
GGAATGATGCGCCTAAGGGTTATCATGGAG
Found at i:6213 original size:19 final size:18
Alignment explanation
Indices: 6180--6215 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6170 TTGAAATAAT
6180 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
6198 TCTTCAGATTATCTTCAA
1 TCTTCA-ATGATCTTCAA
6216 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:6255 original size:51 final size:51
Alignment explanation
Indices: 6189--6305 Score: 225
Period size: 51 Copynumber: 2.3 Consensus size: 51
6179 TTCTTCAATG
6189 ATCTTCAAATCTTCAGATTATCTTCAATAAGTCTTCAAATACGAACTTCGA
1 ATCTTCAAATCTTCAGATTATCTTCAATAAGTCTTCAAATACGAACTTCGA
*
6240 ATCTTCAAATATTCAGATTATCTTCAATAAGTCTTCAAATACGAACTTCGA
1 ATCTTCAAATCTTCAGATTATCTTCAATAAGTCTTCAAATACGAACTTCGA
6291 ATCTTCAAATCTTCA
1 ATCTTCAAATCTTCA
6306 TTCCAAATAG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (51 bp):
ATCTTCAAATCTTCAGATTATCTTCAATAAGTCTTCAAATACGAACTTCGA
Found at i:13084 original size:13 final size:13
Alignment explanation
Indices: 13066--13107 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
13056 TGGCCGGGCA
13066 TGGCCGAGTCATG
1 TGGCCGAGTCATG
*
13079 TGGCCG-GGCA--
1 TGGCCGAGTCATG
13089 TGGCCGAGTCATG
1 TGGCCGAGTCATG
13102 TGGCCG
1 TGGCCG
13108 GGTGTGGCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 6 0.25
11 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.12, C:0.26, G:0.43, T:0.19
Consensus pattern (13 bp):
TGGCCGAGTCATG
Found at i:13114 original size:33 final size:33
Alignment explanation
Indices: 13077--13150 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
13067 GGCCGAGTCA
*
13077 TGTGGCCGGGCATGGCCGA-GTCATGTGGCCGGG
1 TGTGGCCGGGCATGGCC-ATGTCACGTGGCCGGG
* * *
13110 TGTGGCCGGGCATGTCCATGTCGCGTGGCCGGT
1 TGTGGCCGGGCATGGCCATGTCACGTGGCCGGG
13143 TGTGGCCG
1 TGTGGCCG
13151 AGCTCGTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.07, C:0.26, G:0.46, T:0.22
Consensus pattern (33 bp):
TGTGGCCGGGCATGGCCATGTCACGTGGCCGGG
Found at i:13117 original size:23 final size:23
Alignment explanation
Indices: 13054--13109 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
13044 TATGGCCGGT
13054 TGTGGCCGGGCATGGCCGAGTCA
1 TGTGGCCGGGCATGGCCGAGTCA
13077 TGTGGCCGGGCATGGCCGAGTCA
1 TGTGGCCGGGCATGGCCGAGTCA
13100 TGTGGCCGGG
1 TGTGGCCGGG
13110 TGTGGCCGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.11, C:0.25, G:0.46, T:0.18
Consensus pattern (23 bp):
TGTGGCCGGGCATGGCCGAGTCA
Done.